Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000403.1 Corchorus capsularis cultivar CVL-1 contig00403, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6073
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.33
Found at i:228 original size:50 final size:50
Alignment explanation
Indices: 134--352 Score: 212
Period size: 50 Copynumber: 4.4 Consensus size: 50
124 AACTTGTAAA
** * * *
134 TAAAAGATTGAAGCTTTAAATAACT--TAAGTAAAAATGTCATCTTTGGG
1 TAAAAGATTGAATTTTTAAGTAATTAGTAAGTAAAAATGTCATCTTTGAG
* *
182 TAAAAGATTGAATTTTTAAGTAATTAGTAGGTAAAAATGTCATCTTTGGGG
1 TAAAAGATTGAATTTTTAAGTAATTAGTAAGTAAAAATGTCATCTTT-GAG
** *
233 TAAAAGATTGAAACTTT-AGTAATTAGTAAGTAAAGATGTCA-CTTTTGAG
1 TAAAAGATTGAATTTTTAAGTAATTAGTAAGTAAAAATGTCATC-TTTGAG
* * * * * * *
282 CAAAAGATTGATTTTTTTAGAGTAATTAGTAAGTAGAGATGTAACCTTTGAA
1 TAAAAGATTGA-ATTTTTA-AGTAATTAGTAAGTAAAAATGTCATCTTTGAG
*
334 TAAAAGATTGAAGTTTTAA
1 TAAAAGATTGAATTTTTAA
353 AAAGTAATTT
Statistics
Matches: 143, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
48 21 0.15
49 13 0.09
50 48 0.34
51 23 0.16
52 37 0.26
53 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (50 bp):
TAAAAGATTGAATTTTTAAGTAATTAGTAAGTAAAAATGTCATCTTTGAG
Found at i:1290 original size:55 final size:55
Alignment explanation
Indices: 1230--1371 Score: 221
Period size: 55 Copynumber: 2.6 Consensus size: 55
1220 TAAAAGGGGC
1230 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAATAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAATAATAGTAATCAGTA
* **
1285 AATCAGTAATTAAGTAAAAAGAGATTAATAAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAATAATAGTAATCAGTA
* * * *
1340 AATCAGTAATCAGGTAAAAAGATAGTAATCAG
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAG
1372 TAAATTGATT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 79 1.00
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAATAATAGTAATCAGTA
Found at i:1710 original size:21 final size:21
Alignment explanation
Indices: 1651--1982 Score: 205
Period size: 21 Copynumber: 15.2 Consensus size: 21
1641 ATTAGTAAAG
1651 AGTAAAATAGTAAGAAGGTAATC
1 AGTAAAA-AGTAA-AAGGTAATC
* * *
1674 A--ACAAGAGTAAAATAGTAGTC
1 AGTA-AAAAGTAAAA-GGTAATC
1695 AGTAAAAAGTAAATA-GTAATC
1 AGTAAAAAGTAAA-AGGTAATC
* *
1716 AGT-AAGAGTAAAATAGTAATC
1 AGTAAAAAGTAAAA-GGTAATC
* *
1737 AGTAAGAAGTAAAAGGAAATC
1 AGTAAAAAGTAAAAGGTAATC
* *
1758 AGT-AAGAGTAAAAAGGTGATC
1 AGTAAAAAGT-AAAAGGTAATC
* *
1779 AGTAAAGAGTAAAAAGCTAATC
1 AGTAAAAAGT-AAAAGGTAATC
*
1801 AGTAAGAAGTAAAAGGTAATC
1 AGTAAAAAGTAAAAGGTAATC
* *
1822 AGTAAAAAGCAAAAGGCAATC
1 AGTAAAAAGTAAAAGGTAATC
*
1843 AGTAAAAAGTAAAAGAGTAATG
1 AGTAAAAAGTAAAAG-GTAATC
* *
1865 AGTAAAAACGGAGCAGAAAATAGTAATC
1 AGT-AAAA---AG--TAAAA-GGTAATC
1893 AGTAAAAAGTAAGAAGGTAATC
1 AGTAAAAAGTAA-AAGGTAATC
* *
1915 A--ACAAGAGTAAAATAGTAATC
1 AGTA-AAAAGTAAAA-GGTAATC
* *
1936 AGTACAAAGT-AAAGAATAATC
1 AGTAAAAAGTAAAAG-GTAATC
* *
1957 AGTAAAATAGT-GATGGTAATC
1 AGTAAAA-AGTAAAAGGTAATC
1978 AGTAA
1 AGTAA
1983 TTCAGTAAAA
Statistics
Matches: 244, Mismatches: 40, Indels: 52
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.00
20 17 0.07
21 129 0.53
22 67 0.27
23 10 0.04
24 2 0.01
26 2 0.01
27 4 0.02
28 12 0.05
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.19
Consensus pattern (21 bp):
AGTAAAAAGTAAAAGGTAATC
Found at i:1712 original size:14 final size:13
Alignment explanation
Indices: 1680--1772 Score: 51
Period size: 14 Copynumber: 6.7 Consensus size: 13
1670 AATCAACAAG
*
1680 AGTAAAATAGTAGT
1 AGTAAAA-AGTAAT
1694 CAGTAAAAAGTAAAT
1 -AGTAAAAAGT-AAT
** *
1709 AGTAATCAGTAAG
1 AGTAAAAAGTAAT
1722 AGTAAAATAGTAAT
1 AGTAAAA-AGTAAT
* *
1736 CAGTAAGAAGTAAA
1 -AGTAAAAAGTAAT
* * *
1750 AGGAAATCAGTAAG
1 AGTAAA-AAGTAAT
1764 AGTAAAAAG
1 AGTAAAAAG
1773 GTGATCAGTA
Statistics
Matches: 59, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
13 13 0.22
14 31 0.53
15 15 0.25
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.20
Consensus pattern (13 bp):
AGTAAAAAGTAAT
Found at i:1723 original size:42 final size:41
Alignment explanation
Indices: 1651--1872 Score: 230
Period size: 42 Copynumber: 5.2 Consensus size: 41
1641 ATTAGTAAAG
** *
1651 AGTAAAATAGTAAGAAGGTAATCAACAAGAGTAAAATAGTAGTC
1 AGTAAAA-AGTAA-AAGGTAATCAGTAAGAGTAAAA-AGTAATC
1695 AGTAAAAAGTAAATA-GTAATCAGTAAGAGTAAAATAGTAATC
1 AGTAAAAAGTAAA-AGGTAATCAGTAAGAGTAAAA-AGTAATC
* * *
1737 AGTAAGAAGTAAAAGGAAATCAGTAAGAGTAAAAAGGTGATC
1 AGTAAAAAGTAAAAGGTAATCAGTAAGAGTAAAAA-GTAATC
* * *
1779 AGTAAAGAGTAAAAAGCTAATCAGTAAGAAGTAAAAGGTAATC
1 AGTAAAAAGT-AAAAGGTAATCAGTAAG-AGTAAAAAGTAATC
* * * *
1822 AGTAAAAAGCAAAAGGCAATCAGTAAAAAGTAAAAGAGTAATG
1 AGTAAAAAGTAAAAGGTAATCAGT-AAGAGTAAAA-AGTAATC
1865 AGTAAAAA
1 AGTAAAAA
1873 CGGAGCAGAA
Statistics
Matches: 152, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.01
42 87 0.57
43 49 0.32
44 14 0.09
ACGTcount: A:0.55, C:0.06, G:0.21, T:0.18
Consensus pattern (41 bp):
AGTAAAAAGTAAAAGGTAATCAGTAAGAGTAAAAAGTAATC
Found at i:1800 original size:64 final size:64
Alignment explanation
Indices: 1693--1869 Score: 209
Period size: 64 Copynumber: 2.8 Consensus size: 64
1683 AAAATAGTAG
* * *
1693 TCAGTAAAAAGTAAATA-GTAATCAGT-AAGAGTAAAATAGTAATCAGTAAGAAGTAAAAGGAAA
1 TCAGTAAAAAG-AAAAAGGCAATCAGTAAAGAGTAAAAGAGTAATCAGTAAGAAGTAAAAGGAAA
* ** *
1756 TCAGT-AAGAGTAAAAAGGTGATCAGTAAAGAGTAAAA-AGCTAATCAGTAAGAAGTAAAAGGTA
1 TCAGTAAAAAG-AAAAAGGCAATCAGTAAAGAGTAAAAGAG-TAATCAGTAAGAAGTAAAAGGAA
1819 A
64 A
* * *
1820 TCAGTAAAAAGCAAAAGGCAATCAGTAAAAAGTAAAAGAGTAATGAGTAA
1 TCAGTAAAAAGAAAAAGGCAATCAGTAAAGAGTAAAAGAGTAATCAGTAA
1870 AAACGGAGCA
Statistics
Matches: 99, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
62 9 0.09
63 15 0.15
64 69 0.70
65 6 0.06
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (64 bp):
TCAGTAAAAAGAAAAAGGCAATCAGTAAAGAGTAAAAGAGTAATCAGTAAGAAGTAAAAGGAAA
Found at i:2818 original size:18 final size:20
Alignment explanation
Indices: 2797--2840 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
2787 AAAATGTTAG
2797 ATTTAAATTAA-TTTGGA-A
1 ATTTAAATTAACTTTGGACA
**
2815 ATTTAGTTTAACTTTGGACA
1 ATTTAAATTAACTTTGGACA
2835 ATTTAA
1 ATTTAA
2841 TAAACTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (20 bp):
ATTTAAATTAACTTTGGACA
Found at i:3359 original size:49 final size:49
Alignment explanation
Indices: 3302--3591 Score: 336
Period size: 49 Copynumber: 5.9 Consensus size: 49
3292 ATTTTTTCGG
* *
3302 TTTTTACCTGCTATCTCCCAAAATGCCCTTTCCGGACGGAAGGCATTTA
1 TTTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
3351 TTTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
1 TTTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
* * * *
3400 CTTTTACCTGCTGTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTG
1 TTTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
* * * * *
3449 TTTTTACCCGTTATTTCCTAAAATGCCCTTCCCAGACGGAAGGCA-CTA
1 TTTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
* * * *
3497 TTTTCA-CTCACTTTTTCCCAAAAGTGCCTTTCCCGGACGGAAGGCACTATT-
1 TTTTTACCT-GCTATTTCCCAAAA-TGCCCTTCCCGGACGGAAGGCA-T-TTA
* * * *
3548 TTTTTACTTG-TTTTTCCTAAAACGCCCCTTCCCGGACGGAAGGC
1 TTTTTACCTGCTATTTCCCAAAATG-CCCTTCCCGGACGGAAGGC
3592 GTTGCTTTTT
Statistics
Matches: 205, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
47 1 0.00
48 16 0.08
49 152 0.74
50 29 0.14
51 5 0.02
52 2 0.01
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (49 bp):
TTTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
Found at i:4247 original size:63 final size:62
Alignment explanation
Indices: 4163--4291 Score: 213
Period size: 63 Copynumber: 2.1 Consensus size: 62
4153 ATAGTCATTA
4163 TAAGATTTATAATCAAAGTGACTAGCTAAAACGACAAGATTAACCAATTCAATTTGTTTAATC
1 TAAGATTTATAATCAAAGTGACTAGCTAAAACGACAAGATTAACCAATTCAATTTGTTTAA-C
* * * *
4226 TAAGATTTATAATCAAAGTGACTAGCTAAACCGGCAAGATTAGCCAATTCAATTTTTTTAAC
1 TAAGATTTATAATCAAAGTGACTAGCTAAAACGACAAGATTAACCAATTCAATTTGTTTAAC
4288 TAAG
1 TAAG
4292 GTTAAGAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
62 5 0.08
63 57 0.92
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (62 bp):
TAAGATTTATAATCAAAGTGACTAGCTAAAACGACAAGATTAACCAATTCAATTTGTTTAAC
Found at i:5993 original size:21 final size:21
Alignment explanation
Indices: 5967--6008 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5957 AGCACAAGTG
*
5967 ACCGGCCATGCGACTTGGAGA
1 ACCGGCCACGCGACTTGGAGA
5988 ACCGGCCACGCGACTTGGAGA
1 ACCGGCCACGCGACTTGGAGA
6009 TGCCCTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.31, G:0.33, T:0.12
Consensus pattern (21 bp):
ACCGGCCACGCGACTTGGAGA
Found at i:6057 original size:33 final size:33
Alignment explanation
Indices: 5988--6071 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
5978 GACTTGGAGA
* *
5988 ACCGGCCACGCGACTTGGAGATGCCCTTGCAAC
1 ACCGGCCACGCGACATGGAGATGCCCTGGCAAC
* *
6021 ACCGGCCATGCGACATGGAGATGCCC-GGCCATC
1 ACCGGCCACGCGACATGGAGATGCCCTGG-CAAC
6054 ACCGGCCACGCGACATGG
1 ACCGGCCACGCGACATGG
6072 CC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
32 1 0.02
33 44 0.98
ACGTcount: A:0.21, C:0.37, G:0.30, T:0.12
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGAGATGCCCTGGCAAC
Done.